How to disable Safari's in-browser pdf viewer and, instead, force download of selected pdf links in macOS Sierra 10.12.3
1. If you have Adobe Reader installed, disable Adobe's pdf viewer browser plug-ins:
a. Open Adobe Reader/Acrobat Pro; go to Preferences -> Internet; under Web Browser Options, uncheck all boxes; confirm preference changes by selecting "OK."
b. Open Safari; go to Preferences -> Security -> Plug-in Settings; in the left column, uncheck boxes next to any Adobe "PDFViewer..." plug-ins.
c. Quit both Adobe and Safari.
d. Open Finder; go to Macintosh HD/Library/Internet Plug-Ins; in that Internet Plug-Ins folder, you should find a few Adobe plug-ins as well as a folder named "Disabled Plug-Ins" (if you do not yet have a Disabled Plug-Ins folder, create one); move both "AdobePDFViewer.plugin" and "AdobePDFViewerNPAPI.plugin" to Disabled Plug-Ins (requires administrator authentication).
2. Use command line to create a defaults plist entry disabling WebKit in-line pdf viewing:
a. Open Terminal (located in your Applications/Utilities folder); copy-and-paste the following text to Terminal
defaults write com.apple.Safari WebKitOmitPDFSupport -bool YES
b. Hit Return to execute the command.
Note: There is no (automatic) confirmation/response after successful entry of the above command. If, however, you wish to check whether the command worked, you may enter the following:
defaults read com.apple.Safari WebKitOmitPDFSupport
If the entry was successfully made, the system will return "1" on the next line (corresponding to the newly-written "YES" boolean key).
3. Restart your computer.
Comment: I also removed the Adobe Application Manager internet plug-in (AdobeAAMDetect.plugin) as part of Steps 1.b and 1.d, above. I am unsure whether leaving the AAM plug-in might affect the outcome.
The foregoing worked for me, running macOS 10.12.3 and Safari 10.0.3.